(1) Background: Endothelial decompensation is a common complication after penetrating keratopathy (PK), while the risk factors for endothelial decompensation after PK have not been fully elucidated. Consequently, we aim to investigate the possible risk factors for endothelial decompensation after PK. (2) Methods: This retrospective study was conducted using the National Health Insurance Research Database (NHIRD) of Taiwan. The main outcome was the development of endothelial decompensation after PK surgery. The effects of potential risk factors were compared between the patients with endothelial decompensation and the patients without endothelial decompensation via Cox proportional hazard regression, which produced the adjusted hazard ratio (aHR) and a 95% confidence interval (CI). (3) Results: Overall, 54 patients developed endothelial decompensation after PK surgery, with a ratio of 16.12 percent. The pre-existing type 2 diabetes mellitus (T2DM) (aHR: 1.924, 95% CI: 1.257–2.533, p = 0.0095) and history of cataract surgery (aHR: 1.687, 95% CI: 1.328–2.440, p = 0.0026) were correlated with the development of endothelial decompensation. In the subgroup analysis, the correlation between a history of cataract surgery and post-PK endothelial decompensation was more prominent in patients older than 60 years compared to their younger counterparts (p = 0.0038). (4) Conclusions: Pre-existing T2DM and a history of cataract surgery are associated with a higher incidence of post-PK endothelial decompensation.